11th International Workshop on Bioinformatics
and Systems Biology (IBSB), Berlin

17 – 20 July 2011



Sunday, 17 July 2011

Location: Berlin Medical Historical Museum of the Charité (Lecture Hall Rui)


16:00  18:00               Registration
17:00 – 17:45               Tours through the Medical Historical Museum of the Charité
18:00 – 18:10               Edda Klipp, Humboldt University Berlin (Germany)
                                   Welcome and Opening Remarks
18:10 – 19:00               James Sharpe, Center for Genomic Regulation, Barcelona (Spain)  
"Atlases, neutral networks and metagraphs:
new approaches to reveal the design space for small dynamical networks
19:00 – 20:00                Pizza and Drinks



Monday, 18 July 2011

Location: Humboldt Graduate School, “Festsaal”, 2nd floor, Luisenstraße 56,

09:00 – 09:30 Manuela Benary, Humboldt University Berlin (Germany)

“Exploring transcriptional regulation and noise in the Interleukin-2 gene



09:30 – 10:00 Anna Lyubetskaya, Boston University (USA)

“Using ChIP-Seq data to study evolution of regulation in

Mycobacterium tuberculosis and related Actinomycetes”


10:00 – 10:30 Timothy Hancock, Kyoto University (Japan)

“Are Features of Biological Networks Spare or Dense?”


10:30 – 11:00 Coffee Break


11:00 – 11:30 Özgur Demir, Free University Berlin (Germany)

“DemQSAR: application to predicting human volume of distribution and

clearance of drugs”


11:30 – 12:00 Antonio Gomes, Boston University (USA)

“Modeling binding site signal as an extreme value problem improves detection

of binding site locations in ChIPseq data of Mycobacterium tuberculosis”


12:30 - 14:00 Lunch break


14:00 – 14:30 Mayumi Kamada, Kyoto University (Japan)

                                 “Prediction of Protein Residue Contacts using Discriminative Random Fields” 

with Mutual Information


14:30 – 15:00 Juliane Zimmermann, Max Delbrück Center for Molecular Medicine

Berlin (Germany); „Modeling the Force-Velocity Relation of Motile Cells”


15:00 – 15:30 Joshua Campbell, Boston University (USA)

“Characterizing the small RNA transcriptome associated with chronic lung

disease using deep sequencing”


16:30 – 19:30 Poster Session with Coffee and Cake



Tuesday, 19 July 2011


09:00 – 09:30 Robert Lehmann, Humboldt University Berlin (Germany)

"Transcriptional reorganization during transition between metabolic strategies

in Synechocystis sp. 6803“


09:30 – 10:00 Stephanie Schneider, Boston University (USA)

"SCOREM: Statistical Consolidation of Redundant Expression Measures”


10:00 – 10:30 Uechi Risa, Kyoto University (Japan)

"Conservation Laws and Symmetries in Nonlinear Competitive Systems”


10:30 – 11:00 Coffee break


11:00 - 11:30 Marvin Jens, Max Delbrück Center for Molecular Medicine Berlin (Germany)

"Why all this RNA? The transcriptome from the perspective of RNA-binding



11:30 – 12:00 Joachim von Eichborn, Charité, Berlin (Germany)

"Cobweb: Interactive visualisation of networks”


12:00 – 12:30 Ichigaku Takigawa, Kyoto University (Japan)

"Mining significant substructure pairs in drug-target networks”


12:30 – 14:00 Lunch


14:00 – 14:30 Jörn Schmiedel, Max Delbrück Center for Molecular Medicine Berlin (Germany);

"Model of miroRNA regulation reveals novel quantitative insights”


14:30 – 15:00 Chia-Ling Huang, Boston University (USA)

"Identifying key regulators in ovarian cancer by analysis of correlated transcription

in context of a literature-derived causal network”


15:00 – 15:30 Dawid Rasinski, Free University Berlin (Germany)

"*SPARROW: A new tool for predicting the secondary structure of proteins”


15:30 – 16:00 John Brothers, Boston University (USA)

"Redefining the ILD and COPD lung transcriptome with next generation



19:00 – 22:00 boat tour on the river Spree with dinner




Wednesday, 20 July 2011


09:00 – 09:30 Matthias König, Humboldt University Berlin (Germany)

"Modeling of human liver metabolism predicts high risk of hypoglycemic

episodes in T2DM”


09:30 – 10:00 Christopher Jacobs, Boston University (USA)

"Exploration of the link between gene evolutionary rate and model-based gene

importance in yeast”


10:00 – 10:30 Thomas Spießer, Humboldt University Berlin (Germany)

"Size regulation is an intrinsic property of growing yeast cells”


10:30 - 11:00 Coffee break


11:00 – 11:30 Yuki Moriya, Kyoto University (Japan)

"Application of the PathPred metabolic pathway prediction tool to finding

enzyme genes in A. thaliana secondary metabolism”


11:30 – 12:00 Orianne Mazemondet, Humboldt University Berlin (Germany)

"Challenges in yeast glycolysis modelling”


12:00 – 12:30 John Farrell, Boston University (USA)

"Unraveling HLA Disease Associations from Genome Scan Data”


12:30 – 14:00 Lunch Break




14:00 – 15:00 Takeyuki Tamura, Kyoto University (Japan)

"Computing Impact Degrees for Multiple Reactions in Metabolic Networks with


15:00 – 15:30 Thomas Handorf, Humboldt University Berlin (Germany)

                                  "Modeling Cancer Signaling: A Boolean Approach”

15:30 – 16:00 Ai Muto, Kyoto University (Japan)

"Extraction of Tandem Reaction Patterns from Metabolic Pathways”


16:00 Final Remarks